As explained in The Binary Data File, all data is saved to a binary disk file. By default, all signals visible in a schematic are saved. That is all signals at the top level of a hierarchy and in all child schematics are saved. Signals inside subcircuits that were not generated by a hierarchical schematic are not saved.
SIMetrix has comprehensive features for changing exactly what data is saved. Some simulations can generate huge amounts of data and with multi-core multi-step simulations, the rate at which the data is created can exceed the performance of the disk system. It is therefore desirable in some cases to reduce the amount of data saved.
For simulations run from the user interface, some of the data handling features are available through the GUI. See User's Manual/Analysis Modes/Data Handling and Keeps.
More comprehensive features are available using .KEEP and .OPTIONS. See .KEEP for full details.
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